[gmx-users] Re: Umbrella Sampling - ligand

[Justin A. Lemkul]

Steven Neumann wrote:
> Dear Gmx Users, Dear Justin,
>  
> I run Umbrella Sampling for my ligand pulling using Justin's 
> Tutorial. Please, see attached my  histogram and PMF profile.
> I know it requires more sampling around distance from 0.8 to 2.5 nm.
> 1) Will more sampling affect the final deltaG which is now around -7.2 
> kcal/mol ? The profile will be more smooth surely... but the value will 
> stay the same I think.

You need more sampling in the region already stated (since there is none there). 
  Otherwise, things look fine.

> 2) Did I run too many simulations as histogram is very dense? Does it 
> have any effect or it is better to stay like this?
>  

You have some windows where the histograms are almost coincident.  I'd 
investigate why that is, because I'm assuming you didn't intend different 
windows to be redundant.  I don't think there's any harm, but you probably ran 
more windows than is necessary.

-Justin

> Please, if you have any more suggestions, I will appreciate.
>  
> Thank you,
>  
> Steven
> 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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